Background: A large number of Patients treated at our hospital for endocarditis have negative cultures. Taking into consideration the fact that many of these Patients receive antibiotics prior to referral, we decided to study culture-negative endocarditis in Pakistan. Methods: The medical records of all Patients admitted to the Aga Khan University Hospital, Pakistan, for the period from 1988 to 2001, with an underlying diagnosis of infective endocarditis (IE) and negative cultures, were reviewed. Results: Of the 159 Patients diagnosed with IE by revised Duke criteria, 86 (54.1%) had persistent negative cultures. More than half of these Patients (52%) had received antibiotics before being referred to our center. Patients with cutture-negative endocarditis were Less likely to be classified as definite endocarditis by revised Duke criteria (p < 0.001, 95% CI 0.07-0.3) or to have large vegetations (p = 0.021, 95% CI 0.05-0.5), and more likely to have a mitral valve prolapse (p = 0.003, 95% CI 1.6-2.3). Definite endocarditis (p = 0.042, 95% CI 1.02-7.4), heart failure (p = 0.008, 95% CI 1.4-12.7), renal failure (p = 0.017, 95% CI 1.16-40.7), embolism (p = 0.019, 95% CI 1.2-38.8), and neurological complications (p = 0.02, 95% CI 1.16-9.2) were associated with an increased mortality. Conclusion: Culture-negative endocarditis is very common among Patients with IE in Pakistan. The presentation, laboratory findings, and complications are similar to those for culture-positive endocarditis. It is postulated that previous antibiotic treatment is the most common cause of culture-negative endocarditis in our hospital.